A species-specific population of arrangements of repetitive elements (REs), called RE arrays, exists in the human and mouse genomes. We developed an RE analytical tool, named REViewer, for visualizing RE occurrences within RE arrays and other genomic regions as an interactive line map. REViewer utilizes an RE reference library which is established with two RE types: 1) REMiner-generated undefined REs and 2) RepeatMasker-derived defined REs. RE occurrences within queries are visualized as a line map using these two RE types. The REViewer's controller provides analytical options, such as zoom, customization of axis unit, and RE type selection. The functionality of REViewer was evaluated using the human chromosome Y sequence. The REViewer is determined to be an efficient tool that facilitates visualization of up to 6000 REs in RE arrays and other genomic regions. The maximum query size is linked to the RE mining tools (e.g., REMiner, RepeatMasker), not to REViewer.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819206 | PMC |
| http://dx.doi.org/10.1016/j.ygeno.2013.07.008 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.
Plant Genome
March 2025
School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK.
Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis).
View Article and Find Full Text PDFChronic viral mimicry induction following p53 loss promotes immune evasion.
Cancer Discov
January 2025
Princess Margaret Cancer Centre, Toronto, ON, Canada.
Epigenetic therapies facilitate transcription of immunogenic repetitive elements that cull cancer cells through 'viral mimicry' responses. Paradoxically, cancer-initiating events also facilitate transcription of repetitive elements. Contributions of repetitive element transcription towards cancer initiation, and the mechanisms by which cancer cells evade lethal viral mimicry responses during tumor initiation remain poorly understood.
View Article and Find Full Text PDFAn appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers.
PLoS One
January 2025
Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam.
The autonomous and active Long-Interspersed Element-1 (LINE-1, L1) and the non-autonomous Alu retrotransposon elements, contributing to 30% of the human genome, are the most abundant repeated sequences. With more than 90% of their sequences being methylated in normal cells, these elements undeniably contribute to the global DNA methylation level and constitute a major part of circulating-cell-free DNA (cfDNA). So far, the hypomethylation status of LINE-1 and Alu in cellular and extracellular DNA has long been considered a prevailing hallmark of ageing-related diseases and cancer.
View Article and Find Full Text PDFLn-MOF in production of durable antimicrobial and UV-Protective fluorescent cotton fabric for potential application in military textiles.
Sci Rep
January 2025
Chemistry Department, Faculty of Science, Helwan University, Ain-Helwan, Cairo, 11795, Egypt.
Industrialization of military textiles faces many challenges and some requirements such as durability, protection and suitability for hostile environment must be provided. Herein, fluorescent protective cotton with ultraviolet radiation (UVR)-protection and antimicrobial property was currently prepared via the immobilization of lanthanide-metal organic framework (Ln-MOF). Cotton fabrics were primarily activated via cationization process with 3-Chloro-2-hydroxypropyltrimethyl ammonium chloride to obtain the cationized cotton (Q-cotton).
View Article and Find Full Text PDFChromosome-level haplotype-resolved genome of the tropical loach (Oreonectes platycephalus).
Sci Data
January 2025
Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
The flat-headed loach (Oreonectes platycephalus) is a small fish inhabiting headwaters of hillstreams of southern China. Its local populations are characterized by low genetic diversity and exceptionally high differentiation, making it an ideal model for studying small population isolates' persistence and adaptive potential. However, the lack of Oreonectes reference genomes limits endeavours toward these ambitions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!